bims-pideca 2025-09-28 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2025–09–28
twenty-six papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

USP10/GSK3B-mediated inhibition of PTEN drives resistance to PI3K inhibitors in breast cancer.
Next-Generation Multiplexed Targeted Proteomics Quantifies Post-Translational Modifications, Compound-Protein Interactions, and Disease Biomarkers with High Throughput.
Principles of protein abundance regulation across single cells in a mammalian tissue.
Decoding Molecular Network Dynamics in Cells: Advances in Multiplexed Live Imaging of Fluorescent Biosensors.
VEGFR2 blockade overcomes acquired KRAS G12D inhibitor resistance driven by PI3Kγ activation.
KBTBD11 loss promotes AKT hyperactivation and therapeutic vulnerability in prostate cancer.
Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting.
CREPE (CREate Primers and Evaluate): A Computational Tool for Large-Scale Primer Design and Specificity Analysis.
Intrabody targeting of insulin receptor pY1150: A novel approach to modulate signaling pathways in colorectal cancer cells.
Ultrasmall Chemogenetic Tags with Group-Transfer Ligands.
Intrinsic heterogeneity of primary cilia revealed through spatial proteomics.
Impaired PTEN Expression in T Cells Drives Resistance to Treg-Mediated Immune Regulation in Multiple Sclerosis.
Lysosomal LRRC8 complex impacts lysosomal pH, morphology, and systemic glucose metabolism.
Lysosomes signal through the epigenome to regulate longevity across generations.
Reprogramming neuroblastoma by diet-enhanced polyamine depletion.
PTEN hamartoma of soft tissue (PHOST) and fibroadipose vascular anomaly (FAVA): a comparative clinicopathologic and molecular analysis.
PTEN Gene and Autism: Genetic Underpinnings and Neurodevelopmental Impacts.
Vascular Organoids Derived from Capillary malformation-induced Pluripotent Stem Cells Exhibit Disease-Relevant Phenotypes.
Automated Image-Based Profiling of Pluripotent Stem Cell Colonies.
Late failure of Everolimus in a patient with tuberous sclerosis complex after 10 years of effective response: an illustrative case.
GTEx pro enables accurate multi-tissue gene expression analysis using robust normalization and batch correction.
RESTRICT-seq enables time-gated CRISPR screens and uncovers novel epigenetic dependencies of SCC resistance.
OncoDB 2.0: a comprehensive platform for integrated pan-cancer omics analysis.
Identifying an optimal perturbation to induce a desired cell state by generative deep learning.
TAZ enhances the activity of the AKT signaling pathway to promote adipogenesis of gADSCs.
A practical guide to spatial transcriptomics: lessons from over 1000 samples.

J Clin Invest. 2025 Sep 23. pii: e180927. [Epub ahead of print]

USP10/GSK3B-mediated inhibition of PTEN drives resistance to PI3K inhibitors in breast cancer.

Nishi Kumari, Sarah Ce Wright, Christopher M Witham, Laia Monserrat, Marta Palafox, John Lalith Charles Richard, Carlotta Costa, Moshe Elkabets, Mark Agostino, Theresa Klemm, Melissa K Eccles, Alexandra Garnham, Ting Wu, Jonas A Nilsson, Nikita Walz, Veena Venugopal, Anthony Cerra, Natali Vasilevski, Stephanie C Bridgeman, Sona Bassi, Azad Saei, Moutaz Helal, Philipp Neundorf, Angela Riedel, Mathias Rosenfeldt, Jespal Gill, Nikolett Pahor, Oliver Hartmann, Jacky Chung, Sachdev S Sidhu, Nina Moderau, Sudhakar Jha, Jordi Rodon, Markus E Diefenbacher, David Komander, Violeta Serra, Pieter Eichhorn.

  Activating mutations in PIK3CA, the gene encoding the catalytic p110-alpha subunit of PI3K, are some of the most frequent genomic alterations in breast cancer. Alpelisib, a small-molecule inhibitor that targets p110-alpha, is a recommended drug for patients with PIK3CA-mutant advanced breast cancer. However, clinical success for PI3K inhibitors has been limited by their narrow therapeutic window. The lipid phosphatase PTEN is a potent tumour suppressor and a major negative regulator of the PI3K pathway. Unsurprisingly, inactivating mutations in PTEN correlate with tumour progression and resistance to PI3K inhibition due to persistent PI3K signalling. Here we demonstrate that PI3K inhibition leads rapidly to the inactivation of PTEN. Using a functional genetic screen we show that this effect is mediated by a USP10-GSK3-B signalling axis, in which USP10 stabilizes GSK3-B resulting in GSK3-B-mediated phosphorylation of the C-terminal tail of PTEN. This phosphorylation inhibits PTEN dimerization and thus prevents its activation. Downregulation of GSK3-B or USP10 re-sensitizes PI3K inhibitor resistant breast cancer models and patient derived organoids to PI3K inhibition and induces tumour regression. Our study establishes that enhancing PTEN activity is a new strategy to treat PIK3CA mutant tumours and provides a strong rationale for pursuing USP10 inhibitors in the clinic.

Keywords:  Breast cancer; Cell biology; Oncology; Signal transduction; Ubiquitin-proteosome system

DOI:  https://doi.org/10.1172/JCI180927
bioRxiv. 2025 Sep 16. pii: 2025.09.10.675380. [Epub ahead of print]

Next-Generation Multiplexed Targeted Proteomics Quantifies Post-Translational Modifications, Compound-Protein Interactions, and Disease Biomarkers with High Throughput.

Steven R Shuken, Geordon A Frere, Charlotte R Beard, Jesse D Canterbury, Nathan R Zuniga, Brandon M Gassaway, Shane L Dawson, Kean Hean Ooi, João A Paulo, M Windy McNerney, Steven P Gygi, Qing Yu.

The GoDig platform enables sensitive, multiplexed targeted pathway proteomics without manual scheduling or synthetic standards. Here we present GoDig 2.0, which increases sample multiplexing to 35-fold, improves time efficiency and reduces scan delays for higher success rates, and allows flexible spectral and elution library generation from different mass spectrometry data types. GoDig 2.0 measures 2.4× more targets than GoDig 1.0, quantifying >99% of 800 peptides in a single run. We compiled a library of 23,989 human phosphorylation sites from a phosphoproteomic dataset and used it to profile kinase signaling differences across cell lines. In human brain tissue, we established a hyperphosphorylated tau assay including pTau127, revealing potential biomarkers for Alzheimer's disease. We also quantified diglycyl-lysine peptides to assess polyubiquitin branching. Finally, we built a library of 20,946 reactive cysteines and profiled covalent compound-protein interactions spanning diverse pathways. GoDig 2.0 enables high-throughput analyses of site-specific protein modifications across many biological contexts.

DOI: https://doi.org/10.1101/2025.09.10.675380
bioRxiv. 2025 Sep 20. pii: 2025.09.17.676955. [Epub ahead of print]

Principles of protein abundance regulation across single cells in a mammalian tissue.

Andrew Leduc, Gergana Shipkovenska, Yanxin Xu, Alexander Franks, Nikolai Slavov.

Protein synthesis and clearance are major regulatory steps of gene expression, but their in vivo regulatory roles across the cells comprising complex tissues remains unexplored. Here, we systematically quantify protein synthesis and clearance across over 4,200 cells from a primary tissue. Through integration with single-cell transcriptomics, we report the first quantitative analysis of how individual cell types regulate their proteomes across the continuum of gene expression. Our analysis quantifies the relative contributions of RNA abundance, translation, and protein clearance to the abundance variation of thousands of proteins. These results reveal an putative organizing principle: The contributions of both translation and protein clearance are linearly dependent on the cell growth rate. Further, we find that some proteins are primarily regulated by one mechanism (RNA abundance, translation, or clearance) across all cell types while the abundances of other proteins is dominated by different regulatory mechanisms across cell types. Our reliable multimodal measurements enabled quantifying and functionally interpreting molecular variation across single cells from the same cell type. The protein-protein correlations are substantially stronger than the mRNA-mRNA ones, which is mediated by protein clearance regulation. The protein-protein correlations are stronger not only for directly interacting proteins but also between functional sets of proteins. Further, these protein correlations allow identifying cell-type specific functional clusters. These clusters vary across cell types, revealing differences in metabolic processes coordination, partially mediated by protein clearance regulation. Our approach provides a scalable multiplexed framework for quantifying the regulatory processes shaping mammalian tissues and reveals organizing principles determining the relative contributions of translation and protein clearance to the proteomes of primary mammalian cells.

DOI: https://doi.org/10.1101/2025.09.17.676955
Biosensors (Basel). 2025 Sep 17. pii: 614. [Epub ahead of print]15(9):

Decoding Molecular Network Dynamics in Cells: Advances in Multiplexed Live Imaging of Fluorescent Biosensors.

Qiaowen Chen, Yichu Xu, Jhen-Wei Wu, Jr-Ming Yang, Chuan-Hsiang Huang.

  Genetically encoded fluorescent protein (FP)-based biosensors have revolutionized cell biology research by enabling real-time monitoring of molecular activities in live cells with exceptional spatial and temporal resolution. Multiplexed biosensing advances this capability by allowing the simultaneous tracking of multiple signaling pathways to uncover network interactions and dynamic coordination. However, challenges in spectral overlap limit broader implementation. Innovative strategies have been devised to address these challenges, including spectral separation through FP palette expansion and novel biosensor designs, temporal differentiation using photochromic or reversibly switching FPs, and spatial segregation of biosensors to specific subcellular regions or through cell barcoding techniques. Combining multiplexed biosensors with artificial intelligence-driven analysis holds great potential for uncovering cellular decision-making processes. Continued innovation in this field will deepen our understanding of molecular networks in cells, with implications for both fundamental biology and therapeutic development.

Keywords:  FRET; fluorescent biosensors; live cell imaging; multiplexing; signaling dynamics; signaling network

DOI:  https://doi.org/10.3390/bios15090614
bioRxiv. 2025 Sep 18. pii: 2025.09.16.676456. [Epub ahead of print]

VEGFR2 blockade overcomes acquired KRAS G12D inhibitor resistance driven by PI3Kγ activation.

Sung-Hyun Hwang, Mingyun Bae, Ji-Won Kim, Seung Yoon Hyun, Kui-Jin Kim, Joshua H Choe, Min Jung Kim, Ji Won Park, Seung-Yong Jeong, Songji Choi, Woochan Park, Jeongmin Seo, Heejung Chae, Minsu Kang, Eun Hee Jung, Koung Jin Suh, Se Hyun Kim, Jin Won Kim, Yu Jung Kim, Jee Hyun Kim, Haeseong Park, Andrew J Aguirre, Eunjung Alice Lee, Ja-Lok Ku, Keun-Wook Lee.

KRAS G12D mutation is a key oncogenic driver in many solid tumors, including pancreatic, gastric, and colorectal cancers. While recent studies have characterized features associated with primary and acquired resistance to KRAS inhibitors, strategies to overcome such resistance, particularly in the context of gastrointestinal cancers, remain underexplored. Here, we have generated nine human gastrointestinal cancer models, including three patient-derived organoids (PDOs), with acquired resistance to the KRAS G12D-selective inhibitor MRTX1133. Using single-cell RNA sequencing analysis, we identified the enrichment of angiogenesis, hypoxia, and epithelial-to-mesenchymal transition (EMT) signatures in the resistant model compared to the parental PDO. Across all resistant models, VEGFA expression and VEGFR2 phosphorylation were uniformly elevated, which were driven by AKT activation and SP1 nuclear translocation. Mechanistic investigations uncovered increased PI3Kγ activity in MRTX1133-resistant models via complex formation of KRAS with p110γ and p101. This leads to an autocrine VEGFA-VEGFR2 signaling loop formation and EMT induction. Therapeutically, the disruption of VEGFA-VEGFR2 signaling restored MRTX1133 sensitivity and inhibited EMT. Furthermore, cancer-endothelial paracrine signaling amplified angiogenesis, hypoxia, and EMT signatures in cancer cells and simultaneously promoted endothelial cell proliferation, reinforcing an adaptive feedback mechanism. In a mouse model of MRTX1133-resistant tumor xenograft, a combination of anti-VEGFR2 therapy and MRTX1133 more effectively reduced tumor growth, angiogenesis, and proliferation markers than monotherapy without significant body weight change. These findings establish VEGFA-VEGFR2 signaling by PI3Kγ activation as a key driver of acquired resistance to KRAS G12D inhibition and provide a rationale for combining VEGFA-VEGFR2 inhibition with KRAS blockade in KRAS-mutant cancers.
Highlight: VEGFA-VEGFR2 signaling activation is a common feature of MRTX1133 resistance in KRAS G12D cancer cells Nuclear translocation of SP1 by AKT activation promotes VEGFA transcription in MRTX1133-resistant modelsInteraction of p110γ-p101 with KRAS activates PI3Kγ in the resistant models VEGFA-VEGFR2 inhibition reverses MRTX1133 resistance in vitro and in vivo.

DOI: https://doi.org/10.1101/2025.09.16.676456
Oncogene. 2025 Sep 23.

KBTBD11 loss promotes AKT hyperactivation and therapeutic vulnerability in prostate cancer.

Haoyue Sheng, Guohai Shi, Yawen Lu, Shengfeng Zheng, Weijie Gu, Dan Xia, Haojie Huang, Dingwei Ye.

PI3K-AKT signaling axis is often aberrantly activated in human cancers including prostate cancer, but the underlying mechanism of deregulation and tactics for effective targeting of this cancer relevant pathway remain poorly understood. Here, we demonstrate that KBTBD11 E3 ubiquitin ligase gene is frequently deleted in human prostate cancers and that KBTBD11 loss augments AKT phosphorylation in prostate cancer cells in culture and in patient samples. We show that KBTBD11 promotes lysine-27-chain polyubiquitination at lysine 8 and 14 on AKT and antagonizes ubiquitin K63 linkage-mediated polyubiquitination and phosphorylation of AKT. KBTBD11 deficiency drove prostate cancer cell growth in vitro and in vivo, but constituted as a therapeutic vulnerability to the selective AKT inhibitor in prostate cancer. Our study identifies lysine-27-chain polyubiquitination as an inhibitory mechanism of AKT activation and nominates KBTBD11 as an intrinsic upstream inhibitor of AKT. Our findings suggest that KBTBD11 deletion could be a biomarker to guide the use of the AKT inhibitors for the effective treatment of cancers such as prostate cancer.

DOI: https://doi.org/10.1038/s41388-025-03576-w
bioRxiv. 2025 Sep 20. pii: 2025.09.19.676866. [Epub ahead of print]

Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting.

Isabella N Grabski, Junsuk Lee, John Blair, Carol Dalgarno, Isabella Mascio, Alexandra Bradu, David A Knowles, Rahul Satija.

Single-cell perturbation dictionaries provide systematic measurements of how cells respond to genetic and chemical perturbations, and create the opportunity to assign causal interpretations to observational data. Here, we introduce RNA fingerprinting, a statistical framework that maps transcriptional responses from new experiments onto reference perturbation dictionaries. RNA fingerprinting learns denoised perturbation "fingerprints" from single-cell data, then probabilistically assigns query cells to one or more candidate perturbations while accounting for uncertainty. We benchmark our method across ground-truth datasets, demonstrating accurate assignments at single-cell resolution, scalability to genome-wide screens, and the ability to resolve combinatorial perturbations. We demonstrate its broad utility across diverse biological settings: identifying context-specific regulators of p53 under ribosomal stress, characterizing drug mechanisms of action and dose-dependent off-target effects, and uncovering cytokine-driven B cell heterogeneity during secondary influenza infection in vivo. Together, these results establish RNA fingerprinting as a versatile framework for interpreting single-cell datasets by linking cellular states to the underlying perturbations which generated them.

DOI: https://doi.org/10.1101/2025.09.19.676866
Genes (Basel). 2025 Sep 10. pii: 1062. [Epub ahead of print]16(9):

CREPE (CREate Primers and Evaluate): A Computational Tool for Large-Scale Primer Design and Specificity Analysis.

Jonathan W Pitsch, Sara A Wirth, Nicole T Costantino, Josh Mejia, Rose M Doss, Ava V A Warren, Jack Ustanik, Xiaoxu Yang, Martin W Breuss.

   BACKGROUND/OBJECTIVES: Polymerase chain reaction (PCR) is ubiquitous in biological research labs, as it is a fast, flexible, and cost-effective technique to amplify a DNA region of interest. However, manual primer design can be an error-prone and time-consuming process depending on the number and composition of target sites. While Primer3 has emerged as an accessible tool to solve some of these issues, additional computational pipelines are required for appropriate scaling. Moreover, this does not replace the manual confirmation of primer specificity (i.e., the assessment of off-targets).
METHODS: To overcome the challenges of large-scale primer design, we fused the functionality of Primer3 and In-Silico PCR (ISPCR); this integrated pipeline, CREPE (CREate Primers and Evaluate), performs primer design and specificity analysis through a custom evaluation script for any given number of target sites at scale.
RESULTS: CREPE's final output summarizes the lead forward and reverse primer pair for each target site, a measure of the likelihood of binding to off-targets, and additional information to aid decision-making. We provide this through a customized workflow for targeted amplicon sequencing (TAS) on a 150 bp paired-end Illumina platform. Experimental testing showed successful amplification for more than 90% of primers deemed acceptable by CREPE.
CONCLUSIONS: We here provide CREPE, a software platform that allows for parallelized primer design for PCR applications and that is optimized for targeted amplicon sequencing.

Keywords:  bioinformatic tool; polymerase chain reaction; primer design; targeted amplicon sequencing

DOI:  https://doi.org/10.3390/genes16091062
Cell Signal. 2025 Sep 19. pii: S0898-6568(25)00558-3. [Epub ahead of print]136 112143

Intrabody targeting of insulin receptor pY1150: A novel approach to modulate signaling pathways in colorectal cancer cells.

Ha Gyeong Shin, Na-Oh Yunn, Ji Woong Kim, Yea Bin Cho, Sung Ho Ryu, Hyunbo Shim, Sukmook Lee.

  The activation of the insulin receptor (IR) is central to the regulation of physiological metabolism, growth, and proliferation, and is associated with various cancers, including colorectal cancer (CRC). Among the tyrosine residues in the intracellular kinase domain of IR, Tyr1150 plays a pivotal role in receptor activation by regulating substrate binding to the kinase active site. In this study, we introduce a novel approach for selectively modulating insulin signaling in CRC through the development of an intrabody targeting phosphorylated Tyr1150 (IR pY1150). Using phage display technology, we isolated a phosphorylation site-specific single-chain variable fragment (scFv), K109.1, from a human scFv antibody library, which specifically binds to IR pY1150. K109.1 was subsequently engineered as an intrabody designed to function within cells. Ectopic expression of K109.1 in CRC cells selectively inhibited insulin-mediated phosphorylation of key downstream effectors, including insulin receptor substrates and Akt, thereby leading to a significant reduction in insulin-dependent glucose uptake. Notably, K109.1 did not affect extracellular signal-regulated kinase phosphorylation or alter cell proliferation, migration, or invasion. We further evaluated K109.1 in BT-474 and HEK293 cells to assess its effects in additional cellular models. In BT-474 breast cancer cells, K109.1 selectively inhibited Akt phosphorylation, while in HEK293 cells it suppressed both Akt and ERK phosphorylation, indicating context-specific signaling responses. Taken together, these findings indicate that intrabody-mediated targeting of IR pY1150 is crucial for regulating glucose metabolism, suggesting that the developed antibody, K109.1, could serve as a tool for modulating insulin-mediated signaling pathways.

Keywords:  Colorectal cancer; Glucose metabolism; Insulin receptor; Intrabody; Tyrosine phosphorylation

DOI:  https://doi.org/10.1016/j.cellsig.2025.112143
Angew Chem Int Ed Engl. 2025 Sep 27. e202506997

Ultrasmall Chemogenetic Tags with Group-Transfer Ligands.

Vedagopuram Sreekanth, Shaimaa H Sindi, Santosh K Chaudhary, Rajaiah Pergu, Prashant Singh, Endri Karaj, Surached Siriwongsup, Jeffrey E Fung, Arghya Deb, Stephan J DeCarlo, Jaron A M Mercer, Kei Yamada, Diego Rodriguez, David R Liu, Amit Choudhary.

  Chemogenetic tags facilitate exploration of activities of a protein-of-interest (POI) that lacks small-molecule ligands; however, most tags are too large for several POIs. Here, we report two ultrasmall chemogenetic tags (mgTag and cTag) of 36 and 50 amino acids (aa) that, to the best of our knowledge, are the smallest. These tags exhibit transferase-type reactivity with their ligands, allowing the attachment of any moiety-of-interest to the tag. cTag utilizes an engineered C1 domain-bearing cysteine that undergoes a group-transfer reaction with its ligand. Likewise, mgTag utilizes an engineered zinc-finger domain-bearing cysteine that undergoes a group-transfer reaction with its molecular glue ligand in the presence of cereblon (CRBN). While the fusion of HaloTag (297 aa) or SNAPTag (182 aa) to the KRASG12D (188 aa) disrupted its growth-signaling pathway, fusion of mgTag or cTag did not, pointing to the importance of tag size. Group-transfer of BRD4 binder to tags appended to Abelson kinase (ABL) induced proximity between ABL and BRD4, resulting in the latter's phosphorylation. Deletion of the transferase-type reactivity reduced phosphorylation levels, suggesting that proximity-inducing chimeras with group-transfer design may be more efficacious. We envision these ultrasmall tags to have wide-ranging applications, including in basic science, biotechnology, and medicine.

Keywords:  C1 domain; Chemogenetic tags; Induced proximity; KRAS signaling; Molecular glue

DOI:  https://doi.org/10.1002/anie.202506997
Cell. 2025 Sep 25. pii: S0092-8674(25)01029-3. [Epub ahead of print]

Intrinsic heterogeneity of primary cilia revealed through spatial proteomics.

Jan N Hansen, Huangqingbo Sun, Konstantin Kahnert, Eini Westenius, Alexandra Johannesson, Carmela Villegas, Trang Le, Kalliopi Tzavlaki, Casper Winsnes, Emmie Pohjanen, Anna Mäkiniemi, Jenny Fall, Frederic Ballllosera Navarro, Anna Bäckström, Cecilia Lindskog, Fredric Johansson, Kalle von Feilitzen, Angelica M Delgado-Vega, Anna Martinez Casals, Diana Mahdessian, Mathias Uhlén, Shu-Hsien Sheu, Anna Lindstrand, Ulrika Axelsson, Emma Lundberg.

  Primary cilia are critical organelles found on most human cells. Their dysfunction is linked to hereditary ciliopathies with a wide phenotypic spectrum. Despite their significance, the specific roles of cilia in different cell types remain poorly understood due to limitations in analyzing ciliary protein composition. We employed antibody-based spatial proteomics to expand the Human Protein Atlas to primary cilia. Our analysis identified the subciliary locations of 715 proteins across three cell lines, examining 128,156 individual cilia. We found that 69% of the ciliary proteome is cell-type specific, and 78% exhibited single-cilia heterogeneity. Our findings portray cilia as sensors tuning their proteome to effectively sense the environment and compute cellular responses. We reveal 91 cilia proteins and found a genetic candidate variant in CREB3 in one clinical case with features overlapping ciliopathy phenotypes. This open, spatial cilia atlas advances research on cilia and ciliopathies.

Keywords:  3D images; cell-type specificity; cellular heterogeneity; cilia; ciliopathies; immunofluorescence microscopy; primary cilia; signaling; signaling microdomains; spatial proteomics

DOI:  https://doi.org/10.1016/j.cell.2025.08.039
Cells. 2025 Sep 16. pii: 1445. [Epub ahead of print]14(18):

Impaired PTEN Expression in T Cells Drives Resistance to Treg-Mediated Immune Regulation in Multiple Sclerosis.

Janine Schlöder, Bettina Trinschek, Felix Luessi, Helmut Jonuleit.

  The regulation of T cell-mediated immune responses is essential for maintaining immune homeostasis and preventing autoimmune diseases. In multiple sclerosis (MS), impaired immunoregulatory control allows autoreactive T cells to persist, as effector T cells (Teff) display reduced susceptibility to regulatory T cells (Treg). This resistance to Treg-mediated tolerance is linked to altered IL-6 signaling and hyperactivation of protein kinase B (PKB/c-Akt). However, the mechanisms leading to increased PKB phosphorylation remain poorly understood. Here, we examined the expression of phosphatase and tensin homolog PTEN, a key phosphatase that negatively regulates PKB/c-Akt activation. We found that PTEN protein expression rapidly declines in activated Teff from MS patients. To clarify whether PTEN downregulation contributes to Treg resistance, we used PTEN-specific siRNA to modulate PTEN expression in Teff from healthy donors. PTEN knockdown resulted in accelerated IL-6 production, enhanced PKB phosphorylation, and reduced responsiveness to Treg-mediated suppression, similar to Treg resistance observed in MS. This study reports disrupted PTEN expression in activated Teff from MS patients. Our findings highlight that PTEN is critical for effective immune regulation of T cells, and suggest its dysregulation contributes to impaired immune tolerance in MS.

Keywords:  CD4+ T cells; IL-6; PKB hyperactivation; PTEN expression; Treg resistance; immune regulation; multiple sclerosis

DOI:  https://doi.org/10.3390/cells14181445
Sci Adv. 2025 Sep 26. 11(39): eadt6366

Lysosomal LRRC8 complex impacts lysosomal pH, morphology, and systemic glucose metabolism.

Ashutosh Kumar, Yonghui Zhao, Litao Xie, Rahul Chadda, John D Tranter, Ryan T Mikami, Nihil Abraham, Juan Hong, Ethan Feng, David R Rawnsley, Haiyan Liu, Kayla M Henry, Gretchen Meyer, Meiqin Hu, Haoxing Xu, Antentor Hinton, Chad E Grueter, E Dale Abel, Andrew W Norris, Abhinav Diwan, Rajan Sah.

The lysosome integrates anabolic signaling and nutrient sensing to regulate intracellular growth pathways. The leucine-rich repeat-containing 8 (LRRC8) channel complex forms a lysosomal anion channel and regulates PI3K-AKT-mTOR signaling, skeletal muscle differentiation, growth, and systemic glucose metabolism. Here, we define the endogenous LRRC8 subunits localized to a subset of lysosomes in differentiated myotubes. We show that LRRC8A affects leucine-stimulated mTOR; lysosome size; number; pH; expression of lysosomal proteins LAMP2, P62, and LC3B; and lysosomal function. Mutating an LRRC8A lysosomal targeting dileucine motif sequence (LRRC8A-L706A;L707A) in myotubes recapitulates the abnormal AKT signaling and altered lysosomal morphology and pH observed in LRRC8A knockout cells. In vivo, LRRC8A-L706A;L707A knock-in mice exhibit increased adiposity, impaired glucose tolerance and insulin resistance associated with reduced skeletal muscle PI3K-AKT-mTOR signaling, glucose uptake, and impaired incorporation of glucose into glycogen. These data reveal a lysosomal LRRC8-mediated metabolic signaling function regulating lysosomal function, systemic glucose homeostasis, and insulin sensitivity.

DOI: https://doi.org/10.1126/sciadv.adt6366
Science. 2025 Sep 25. 389(6767): 1353-1360

Lysosomes signal through the epigenome to regulate longevity across generations.

Qinghao Zhang, Weiwei Dang, Meng C Wang.

The epigenome is sensitive to metabolic inputs and is crucial for aging. Lysosomes act as a signaling hub to sense metabolic cues and regulate longevity. We found that lysosomal metabolic pathways signal through the epigenome to regulate transgenerational longevity in Caenorhabditis elegans. Activation of lysosomal lipid signaling and lysosomal adenosine monophosphate-activated protein kinase (AMPK) or reduction of lysosomal mechanistic target of rapamycin (mTOR) signaling increased the expression of a histone H3.3 variant and increased its methylation on K79, leading to life-span extension across multiple generations. This transgenerational prolongevity effect required intestine-to-germline transportation of histone H3.3 and a germline-specific H3K79 methyltransferase and was recapitulated by overexpressing H3.3 or the H3K79 methyltransferase. Thus, signals from a lysosome affect the epigenome and link the soma and germ line to mediate transgenerational inheritance of longevity.

DOI: https://doi.org/10.1126/science.adn8754
Nature. 2025 Sep 24.

Reprogramming neuroblastoma by diet-enhanced polyamine depletion.

Sarah Cherkaoui, Christina S Turn, Yuan Yuan, Wenyun Lu, Lifeng Yang, Matthew J McBride, Caroline Eigenmann, George E Allen, Olesya O Panasenko, Lu Zhang, Annette Vu, Kangning Liu, Yimei Li, Om H Gandhi, Lea F Surrey, Sandra D Kienast, Sebastian A Leidel, Michael Wierer, Eileen White, Joshua D Rabinowitz, Michael D Hogarty, Raphael J Morscher.

Neuroblastoma is a highly lethal childhood tumour derived from differentiation-arrested neural crest cells1,2. Like all cancers, its growth is fuelled by metabolites obtained from either circulation or local biosynthesis3,4. Neuroblastomas depend on local polyamine biosynthesis, and the inhibitor difluoromethylornithine has shown clinical activity5. Here we show that such inhibition can be augmented by dietary restriction of upstream amino acid substrates, leading to disruption of oncogenic protein translation, tumour differentiation and profound survival gains in the Th-MYCN mouse model. Specifically, an arginine- and proline-free diet decreases the amount of the polyamine precursor ornithine and enhances tumour polyamine depletion by difluoromethylornithine. This polyamine depletion causes ribosome stalling, unexpectedly specifically at codons with adenosine in the third position. Such codons are selectively enriched in cell cycle genes and low in neuronal differentiation genes. Thus, impaired translation of these codons, induced by combined dietary and pharmacological intervention, favours a pro-differentiation proteome. These results suggest that the genes of specific cellular programmes have evolved hallmark codon usage preferences that enable coherent translational rewiring in response to metabolic stresses, and that this process can be targeted to activate differentiation of paediatric cancers.

DOI: https://doi.org/10.1038/s41586-025-09564-0
Virchows Arch. 2025 Sep 26.

PTEN hamartoma of soft tissue (PHOST) and fibroadipose vascular anomaly (FAVA): a comparative clinicopathologic and molecular analysis.

Shuang Xue, Fangfang Fu, Ying Wang, Dakan Liu, Haohui Zhu, Li Xiao, Jing Huang, Qiuyu Liu.

  PTEN hamartoma of soft tissue (PHOST) is a rare entity within the PTEN-related hamartoma tumor syndrome spectrum. It often presents with overlapping clinical features with other vascular anomalies, such as fibroadipose vascular anomaly (FAVA). While both conditions are characterized by intramuscular vascular anomalies, their underlying genetic mutations and histopathological features are distinct. This study aims to elucidate the genetic and clinicopathological characteristics of PHOST, and to compare it with FAVA, highlighting critical diagnostic features. We retrospectively reviewed all cases that underwent surgical treatment in our pathology database from 2021 to 2024 and selected 28 cases with complex vascular malformations, all of which tested negative for PIK3CA mutations by fluorescent quantitative PCR (qPCR). Subsequently, next-generation sequencing (NGS) was performed on these 28 cases to evaluate their mutation profiles. Comprehensive clinicopathological evaluations, including imaging, were conducted. Treatment outcomes and recurrence rates were analyzed during long-term follow-up. The histological and genetic findings were compared between PHOST and FAVA cases. PHOST typically presents with vascular nodules in a fibrous and adipocytic background. It features numerous small vessels resembling arteries and veins, along with indeterminate channels. The presence of larger vessels with arterial-to-venous transitions and thick-walled muscular vessels suggests arteriovenous shunting, a feature absent in FAVA. Unlike PHOST, FAVA cases predominantly harbored PIK3CA mutations and exhibited localized, low-flow vascular anomalies. Detecting PTEN gene mutations in complex vascular malformations is crucial for the accurate diagnosis of PHOST. This study underscores the importance of genetic testing and tailored therapeutic approaches for these rare vascular anomalies.

Keywords:   PIK3CA ; PTEN ; Fibro-adipose vascular anomaly; PTEN hamartoma of soft tissue; Vascular anomaly

DOI:  https://doi.org/10.1007/s00428-025-04273-5
Genes (Basel). 2025 Sep 09. pii: 1061. [Epub ahead of print]16(9):

PTEN Gene and Autism: Genetic Underpinnings and Neurodevelopmental Impacts.

Ann C Genovese, Merlin G Butler.

  Background/Objectives: Twin and family studies suggest that 90% of the risk for autism spectrum disorder (ASD) is due to genetic factors, with 800 genes recognized as playing a role. An important gene is phosphatase and tensin homolog (PTEN), which plays a significant role in cancer as a tumor suppressor best known for causing overgrowth and PTEN hamartoma tumor syndromes (PHTS). Less well known are PTEN germline mutations with adverse neurodevelopmental impacts of macrocephaly, intellectual disability, and ASD, as well as other behavioral and psychiatric disturbances. There remains a limited understanding of whether these gene variants are associated with differing manifestations of PTEN-associated neurodevelopmental disorders. Methods: This review utilized comprehensive literature searches such as PubMed, OMIM, and Gene Reviews with keywords of PTEN, genetic factors, autism, and human studies and by searching genomic-protein functional networks with STRING computer-based programs for functional and genetic mechanisms. Results: This review explored the genetic underpinnings of PTEN gene variants causing altered interactive proteins and their mechanisms, biological processes, molecular functions, pathways, and disease-gene associations. We characterized specific gene-gene or protein-protein interactions and their functions relating to neurodevelopment, psychiatric disorders, and ASD that were found to be increased with PTEN gene variants. Conclusions: PTEN gene defects are among the most recognized genetic causes of ASD. PTEN gene variants and altered protein interactions and mechanisms described in our study are associated with an increased risk for tissue and organ overgrowth, macrocephaly, and distinct brain anomalies, specifically newly identified abnormal CSF dynamics. These genetic underpinnings and impacts on neurodevelopment are discussed. The genetic and protein findings identified may offer clues to effective treatment interventions, particularly when instituted at a young age, to improve long-term outcomes.

Keywords:  ASD; PTEN gene; abnormal CSF dynamics; autism; genetic functions and mechanisms; macrocephaly; neurodevelopment; protein interactions

DOI:  https://doi.org/10.3390/genes16091061
Stem Cell Rev Rep. 2025 Sep 25.

Vascular Organoids Derived from Capillary malformation-induced Pluripotent Stem Cells Exhibit Disease-Relevant Phenotypes.

Vi Nguyen, Anna Harper, Mackenzie Azuero, Isabella Castellanos, Siwuxie He, Marcelo L Hochman, Camilla F Wenceslau, Dong-Bao Chen, Anil G Jegga, Yunguan Wang, Daping Fan, J Stuart Nelson, Wenbin Tan.

  Capillary malformation (CM) is a congenital vascular anomaly that affects the skin, mucosa, eye, and brain. A major obstacle to mechanistic and drug screening studies for CM has been the lack of preclinical models. In this study, we established vascular organoids (VOs) generated through the self-assembly of vascular lineages of endothelial cells and smooth muscle cells differentiated from CM-induced pluripotent stem cells (iPSC). Within these VOs induced endothelial cells and smooth muscle cells organized into juxtapositions to form vascular branches. CM patient iPSC-derived VOs showed a higher density of endothelial and smooth muscle cell populations and greater vascular branch lengths as compared with VOs derived from iPSCs generated from healthy skin biopsies. Overall, this study represents the first disease-relevant VO model of CM, providing a valuable platform for future mechanistic studies and drug screening.

Keywords:  Capillary Malformation; Endothelial Cells; Human Induced Pluripotent Stem Cells; Smooth Muscle Cells; Vascular Organoid

DOI:  https://doi.org/10.1007/s12015-025-10984-8
bioRxiv. 2025 Sep 16. pii: 2025.09.16.676586. [Epub ahead of print]

Automated Image-Based Profiling of Pluripotent Stem Cell Colonies.

Rui Geng, Benjamin L Kidder.

Quantitative image analysis is essential for advancing stem cell biology, developmental studies, and drug discovery, yet most workflows still rely on manual or semi-quantitative scoring that is slow, subjective, and poorly scalable. A major challenge is converting complex colony morphologies into reproducible, high-dimensional datasets. To address this gap, we developed ColonyQuant , an open-source platform that integrates automated colony segmentation, alkaline phosphatase (AP) intensity quantification, morphometric profiling, and statistical classification into a single workflow. ColonyQuant computes per-colony functional readouts alongside comprehensive shape descriptors, capturing both staining intensity and structural features in a unified framework. Applied to embryonic stem cells (ESCs) treated with a selective KDM4 histone-demethylase inhibitor, ColonyQuant revealed dose-dependent reductions in colony area and integrated AP signal, together with systematic remodeling of morphometric metrics. Multivariate analyses robustly stratified treatment groups and identified intensity and solidity as principal features capturing dose-dependent colony responses. By transforming subjective scoring into objective, scalable, and biologically interpretable phenotyping, ColonyQuant provides a reproducible platform for stem cell research and high-content screening.

DOI: https://doi.org/10.1101/2025.09.16.676586
Childs Nerv Syst. 2025 Sep 25. 41(1): 294

Late failure of Everolimus in a patient with tuberous sclerosis complex after 10 years of effective response: an illustrative case.

Carla Richetta, Shlomi Constantini, Rina Dvir, Jonathan Roth.

   INTRODUCTION AND PURPOSE: Late treatment failure following an initially effective response to targeted therapy may occur. Everolimus, a targeted drug that serves as an mTOR (rapamycin) inhibitor, has been extensively studied for its efficacy and safety in treating subependymal giant cell astrocytomas (SEGA) in pediatric patients with tuberous sclerosis complex (TSC). Clinical studies have demonstrated that Everolimus leads to a sustained reduction in SEGA volume. However, TSC patients may need to continue long term or even lifelong treatment to avoid the risk of progression following termination of treatment. The case report provided here demonstrates that late failure can occur even while in treatment.
CASE REPORT: We hereby describe a 16-year-old female diagnosed with TSC and bilateral large intraventricular SEGA, who displayed sustained tumor volume reduction on Everolimus treatment for 10 years. Despite proper adjustment of dosage, confirmed by blood levels, the lesions eventually grew. This bilateral tumor growth subsequently led to symptomatic hydrocephalus. Therefore, at this point, the Everolimus treatment was stopped, and the girl was operated upon. Following subtotal surgical resection, a decision was made to simply follow the residual tumor remnant. When, after a few months, the tumor remnant was found to be slowly growing, the patient was re-started on Everolimus, which proved again to be effective in stabilizing the lesion growth.
DISCUSSION: Everolimus is a well-known treatment for patients affected by TSC-related SEGA. Maintenance therapy can be continued safely for prolonged periods with continuous tumor volume stability. Nonetheless, late failure of treatment may still occur and require surgery. Potential mechanisms of such late reduction in effectiveness are discussed.

Keywords:  Everolimus; Late failure; SEGA; TSC

DOI:  https://doi.org/10.1007/s00381-025-06959-2
Sci Rep. 2025 Sep 23. 15(1): 32684

GTEx pro enables accurate multi-tissue gene expression analysis using robust normalization and batch correction.

D Jothi.

The Genotype-Tissue Expression (GTEx) project provides a valuable resource for investigating gene regulation across various human tissues. However, its cross-sectional design introduces technical artifacts and batch effects related to donor demographics and tissue processing. These confounders obscure biological signals and distort multi-tissue analyses. We present GTEx_Pro, a Nextflow-based pipeline for preprocessing GTEx v8 transcriptomic data, enhancing multi-tissue comparability. It integrates TMM + CPM normalization and SVA batch effect correction to improve biological signal recovery while reducing systematic variations across 54 GTEx tissues. Designed for scalability and reproducibility, GTEx_Pro facilitates accurate multi-tissue transcriptomic analysis, and a similar framework can be adapted to other large-scale transcriptome datasets.

DOI: https://doi.org/10.1038/s41598-025-20697-0
bioRxiv. 2025 Sep 20. pii: 2025.09.17.676440. [Epub ahead of print]

RESTRICT-seq enables time-gated CRISPR screens and uncovers novel epigenetic dependencies of SCC resistance.

Selahattin Can Ozcan, Dreyton G Amador, Justin Anthony Powers, Ashley G Njiru, Zahra Ansari, Yvon Woappi.

Cancer cell evasion of therapy is a highly adaptive process that undermines the efficacy of many treatment strategies. A significant milestone in the study of these mechanisms has been the advent of pooled CRISPR knockout screens, which enable high-throughput, genome-wide interrogations of tumor dependencies and synthetic lethal interactions, advancing our understanding of how cancer cells adapt to and evade therapies. However, the utility of this approach diminishes when applied to dynamic biological contexts, where processes are transient and sensitivity to routine cell culture manipulations that introduce noise and limit meaningful discoveries. To overcome these limitations, we present RESTRICT-seq, a next-generation pooled screening methodology that restricts Cas9 nuclear activation in controlled, repeated cycles. By confining Cas9 catalytic activity to strict temporal windows, RESTRICT-seq mitigates undesired fitness penalties that routinely accumulate throughout pooled screens. When benchmarked against conventional pooled screens and standard inducible protocols, RESTRICT-seq revealed significantly fewer divergent cell clones and increased signal-to-noise ratio, overcoming a key limitation of traditional methods. Leveraging RESTRICT-seq, we conducted a comprehensive functional survey of the druggable mammalian epigenome, uncovering several elusive epigenetic drivers of treatment resistance in cutaneous squamous cell carcinoma (cSCC). This revealed PAK1 as a previously unrecognized mediator of cSCC resistance in human and mouse SCC, offering new insights into a prognostic marker and therapeutic target of high clinical significance. Our findings establish RESTRICT-seq as a powerful tool for extending the applicability of pooled CRISPR screens to dynamic and previously intractable biological contexts.

DOI: https://doi.org/10.1101/2025.09.17.676440
Nucleic Acids Res. 2025 Sep 23. pii: gkaf952. [Epub ahead of print]

OncoDB 2.0: a comprehensive platform for integrated pan-cancer omics analysis.

Minsu Cho, Gongyu Tang, Charles S Rogers, Makayla Dove, Xinyi Liu, Yuanxiang Li, Xiaowei Wang.

OncoDB was initially developed to advance cancer research by integrating RNA expression profiles, DNA methylation patterns, clinical annotations, and oncoviral signatures derived from the Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression datasets. We now present OncoDB 2.0, an extensively expanded platform that offers a more comprehensive and integrated view of cancer omics. The updated version includes an atlas of somatic mutations discovered from combined DNA and RNA sequencing, enabling in-depth investigation of mutation patterns across tumor types and their association with clinical features. Furthermore, we have integrated proteomic data from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and chromatin accessibility data from TCGA, offering new dimensions for oncogene regulation studies. OncoDB 2.0 also introduces advanced multi-omics analysis modules that facilitate the combined exploration of RNA expression, DNA methylation, and somatic mutations, allowing researchers to examine complex cross-omic relationships with greater depth and flexibility. Together, these enhancements make OncoDB 2.0 a robust and invaluable tool for the cancer research community. OncoDB 2.0 is freely available at https://oncodb.org.

DOI: https://doi.org/10.1093/nar/gkaf952
Cell Syst. 2025 Sep 24. pii: S2405-4712(25)00238-8. [Epub ahead of print] 101405

Identifying an optimal perturbation to induce a desired cell state by generative deep learning.

Younghyun Han, Hyunjin Kim, Chun-Kyung Lee, Kwang-Hyun Cho.

  Controlling cell states is pivotal in biological research, yet understanding the specific perturbations that induce desired changes remains challenging. To address this, we present PAIRING (perturbation identifier to induce desired cell states using generative deep learning), which identifies cellular perturbations leading to the desired cell state. PAIRING embeds cell states in the latent space and decomposes them into basal states and perturbation effects. The identification of optimal perturbations is achieved by comparing the decomposed perturbation effects with the vector representing the transition toward the desired cell state in the latent space. We demonstrate that PAIRING can identify perturbations transforming given cell states into desired states across different types of transcriptome datasets. PAIRING is employed to identify perturbations that lead colorectal cancer cells to a normal-like state. Moreover, simulating gene expression changes using PAIRING provides mechanistic insights into the perturbation. We anticipate that it will have a broad impact on therapeutic development, potentially applicable across various biological domains.

Keywords:  cell state control; computational biology; deep learning; perturbation identification; systems biology

DOI:  https://doi.org/10.1016/j.cels.2025.101405
Stem Cell Res Ther. 2025 Sep 26. 16(1): 516

TAZ enhances the activity of the AKT signaling pathway to promote adipogenesis of gADSCs.

Mei Zhou, Hongyan Zhang, Xiong Miao, Ying Zhao, Long Zhu, Jie Liu, Dongjun Liu.

  Adipose-derived mesenchymal stem cells (ADSCs) possess the capacity for multidirectional differentiation, including differentiation into adipocytes. However, the molecular mechanisms that control adipogenesis are not yet fully understood.Transcriptional co-activator with PDZ-binding motif (TAZ) can act as a molecular rheostat, finely regulating the balance between osteoblast and adipocyte differentiation. In this study, we investigated whether TAZ plays a role in the adipogenesis of goat ADSCs (gADCS). Our results indicated that the expression of TAZ increased during adipogenesis of gADSCs. We established gADSCs cell lines with stable TAZ overexpression and knockdown. We found that TAZ overexpression promoted the adipogenesis of gADSCs, whereas its knockdown inhibited this process. Furthermore, TAZ overexpression and knockdown altered the nuclear expression of Yes-associated protein(YAP) and TAZ. Subsequent analyses indicated that TAZ overexpression increased AKT phosphorylation levels. Moreover, treatment with a PI3K inhibitor (LY294002) abrogated the TAZ-induced increase in adipogenesis, suggesting that TAZ regulates the adipogenesis of gADSCs via the PI3K/AKT pathway. Collectively, our results indicate that TAZ promotes the adipogenesis of gADSCs by enhancing the activity of the PI3K/AKT signaling pathway.

Keywords:  Adipogenesis; Adipose mesenchymal stem cells; PI3K/AKT; TAZ

DOI:  https://doi.org/10.1186/s13287-025-04640-8
Trends Biotechnol. 2025 Sep 19. pii: S0167-7799(25)00357-9. [Epub ahead of print]

A practical guide to spatial transcriptomics: lessons from over 1000 samples.

Daniela Grases, Eduard Porta-Pardo.

  Spatial transcriptomics (ST) enables the  in situ mapping of gene expression, revolutionizing our ability to study tissue organization and cellular interactions. However, many groups struggle with practical barriers to implementation, including platform selection, sample quality, and experimental scalability. We provide a practical guide to ST, informed by the processing and analysis of over 1000 spatial samples across multiple ST platforms. We outline best practices for experimental design, tissue handling, sequencing, and computational analysis, with special attention to clinical samples. Our goal is to translate hands-on experience into recommendations that support robust, reproducible spatial workflows. This guide is designed to assist researchers at all levels: from those designing their first spatial experiment to groups aiming to integrate ST into large-scale studies.

Keywords:  Visium; Xenium; best practices; experimental design; spatial omics; spatial transcriptomics

DOI:  https://doi.org/10.1016/j.tibtech.2025.08.020